Title

Structural segments and residue propensities in protein-RNA interfaces: Comparison with protein-protein and protein-DNA complexes

Authors

Sumit Biswas¹, Mainak Guharoy¹ and Pinak Chakrabarti^1, *

Affiliation

¹Department of Biochemistry and Bioinformatics Centre, Bose Institute, Kolkata 700054, India

Email

pinak@boseinst.ernet.in; * Corresponding author

91 33 2355 0256

91 33 2355 3886

Article Type

Hypothesis

Date

received May 23, 2008; revised June 19, 2008; accepted July 07, 2008; published July 14, 2008

Abstract

The interface of a protein molecule that is involved in binding another protein, DNA or RNA has been characterized in terms of the number of unique secondary structural segments (SSSs), made up of stretches of helix, strand and non-regular (NR) regions. On average 10-11 segments define the protein interface in protein-protein (PP) and protein-DNA (PD) complexes, while the number is higher (14) for protein-RNA (PR) complexes.  While the length of helical segments in PP interaction increases with the interface area, this is not the case in PD and PR complexes. The propensities of residues to occur in the three types of secondary structural elements (SSEs) in the interface relative to the corresponding elements in the protein tertiary structures have been calculated. Arg, Lys, Asn, Tyr, His and Gln are preferred residues in PR complexes; in addition, Ser and Thr are also favoured in PD interfaces.

Keywords

protein-protein interactions; DNA; RNA interactions; binding interface; protein secondary structure

Citation

Biswas et al., Bioinformation 2(10): 422-427 (2008)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.